The management of children with pediatric mastocytosis poses a challenge. There is a limited information as to the application of clinical and laboratory findings and bone marrow evaluation as they relate to medical intervention and prognosis. The diagnostic criteria for pediatric mastocytosis are largely based on adult studies. There is very little data about bone marrow pathology in children with mastocytosis. We evaluated the use of the World Health Organization (WHO) criteria for the diagnosis of systemic disease in pediatric patients. Bone marrow biopsies were analyzed by histopathology and immunohistochemistry, flow cytometry and KIT mutational analysis. Complete bone marrow evaluations were performed in 50 cases. Seven children had repeat procedures. We identified unique clinico-histopathological features within the biopsies. Bone marrow biopsies displayed mildly atypical hematopoietic maturation, increased hematogones and hypocellularity in a sub-set of patients with urticaria pigmentosa, diffuse cutaneous mastocytosis and indolent systemic mastocytosis. Hypocellularity was most pronounced in those with urticaria pigmentosa. Hematogone increases were highest, on average, in patients with diffuse cutaneous mastocytosis or mastocytomas. There was no evidence of peripheral blood cytopenias, myelodysplastic syndrome, myeloproliferative neoplasm or leukaemia within this cohort. Long-term follow-up of patients within this study (median 6.9 years; range 1-25 years) showed that all patients remained clinically stable without progression to a more aggressive variant. We conclude that the WHO criteria are applicable for the diagnosis of systemic mastocytosis in pediatrics.